Over the years it has become necessary for antivirus software to check an increasing variety of files, rather than just executables, for several reasons:

Powerful macros used in word processor applications, such as Microsoft Word, presented a risk. Virus writers could use the macros to write viruses embedded within documents. This meant that computers could now also be at risk from infection by opening documents with hidden attached macros.

Later email programs, in particular Microsoft's Outlook Express and Outlook, were vulnerable to viruses embedded in the email body itself. A user's computer could be infected by just opening or previewing a message.
As always-on broadband connections became the norm, and more and more viruses were released, it became essential to update virus checkers more and more frequently.

There are several methods which antivirus software can use to identify malware.
Signature based detection is the most common method. To identify viruses and other malware, antivirus software compares the contents of a file to a dictionary of virus signatures. Because viruses can embed themselves in existing files, the entire file is searched, not just as a whole, but also in pieces.

Heuristic-based detection, like malicious activity detection, can be used to identify unknown viruses.

File emulation is another heuristic approach. File emulation involves executing a program in avirtual environment and logging what actions the program performs. Depending on the actions logged, the antivirus software can determine if the program is malicious or not and then carry out the appropriate disinfection actions.
Traditionally, antivirus software heavily relied upon signatures to identify malware. This can be very effective, but cannot defend against malware unless samples have already been obtained and signatures created. Because of this, signature-based approaches are not effective against new, unknown viruses.

As new viruses are being created each day, the signature-based detection approach requires frequent updates of the virus signature dictionary. To assist the antivirus software companies, the software may allow the user to upload new viruses or variants to the company, allowing the virus to be analyzed and the signature added to the dictionary.

Although the signature-based approach can effectively contain virus outbreaks, virus authors have tried to stay a step ahead of such software by writing "oligomorphic", "polymorphic" and, more recently, "metamorphic" viruses, which encrypt parts of themselves or otherwise modify themselves as a method of disguise, so as to not match virus signatures in the dictionary.

Some more sophisticated antivirus software uses heuristic analysis to identify new malware or variants of known malware.

Many viruses start as a single infection and through either mutation or refinements by other attackers, can grow into dozens of slightly different strains, called variants. Generic detection refers to the detection and removal of multiple threats using a single virus definition.

For example, the Vundo trojan has several family members, depending on the antivirus vendor's classification. Symantec classifies members of the Vundo family into two distinct categories, Trojan.Vundo and Trojan.Vundo.B.

While it may be advantageous to identify a specific virus, it can be quicker to detect a virus family through a generic signature or through an inexact match to an existing signature. Virus researchers find common areas that all viruses in a family share uniquely and can thus create a single generic signature. These signatures often contain non-contiguous code, using wildcard characters where differences lie. These wildcards allow the scanner to detect viruses even if they are padded with extra, meaningless code. A detection that uses this method is said to be "heuristic detection."

Rootkit detection
Anti-virus software can also scan for rootkits; a rootkit is a type of malware that is designed to gain administrative-level control over a computer system without being detected. Rootkits can change how the operating system functions and in some cases can tamper with the anti-virus program and render it ineffective. Rootkits are also difficult to remove, in some cases requiring a complete re-installation of the operating system.

Issues of concern renewal
Some commercial antivirus software end-user license agreements include a clause that the subscription will be automatically renewed, and the purchaser's credit card automatically billed, at the renewal time without explicit approval.

System and interoperability related issues
Running multiple antivirus programs concurrently can degrade performance and create conflicts. However, using a concept calledmultiscanning, several companies (including G Data and Microsoft  have created applications which can run multiple engines concurrently.

It is sometimes necessary to temporarily disable virus protection when installing major updates such as Windows Service Packs or updating graphics card drivers. Active antivirus protection may partially or completely prevent the installation of a major update.

Active anti-virus programs can cause conflicts with other programs. For example, the True Crypt troubleshooting page reports that anti-virus programs are known to conflict with True Crypt and cause it to malfunction.

 Support issues also exist around antivirus application interoperability with common solutions like SSL VPN remote access and network access control products. These technology solutions often have policy assessment applications which require that an up to date antivirus is installed and running. If the antivirus application is not recognized by the policy assessment, whether because the antivirus application has been updated or because it is not part of the policy assessment library, the user will be unable to connect.

The problem is magnified by the changing intent of virus authors. Some years ago it was obvious when a virus infection was present. The viruses of the day, written by amateurs, exhibited destructive behavior or pop-ups. Modern viruses are often written by professionals, financed by criminal organizations.

 Independent testing on all the major virus scanners consistently shows that none provide 100% virus detection. The best ones provided as high as 99.6% detection, while the lowest provided only 81.8% in tests conducted in February 2010. All virus scanners produce false positive results as well, identifying benign files as malware.

New viruses
Most popular anti-virus programs are not very effective against new viruses, even those that use non-signature-based methods that should detect new viruses. The reason for this is that the virus designers test their new viruses on the major anti-virus applications to make sure that they are not detected before releasing them into the wild.
 Some new viruses, particularly ransom ware, use polymorphic code to avoid detection by virus scanners. Jerome Segura, a security analyst with Proctologic, explained.

It's something that they miss a lot of the time because this type of [ransom ware virus] comes from sites that use a polymorphism, which means they basically randomize the file they send you and it gets by well-known antivirus products very easily. I've seen people firsthand getting infected, having all the pop-ups and yet they have antivirus software running and it's not detecting anything. It actually can be pretty hard to get rid of, as well, and you're never really sure if it's really gone. When we see something like that usually we advise to reinstall the operating system or reinstall backups

A proof of concept malware has shown how new viruses could use the Graphics Processing Unit (GPU) to avoid detection from anti-virus software. The potential success of this involves bypassing the CPU in order to make it much harder for security researchers to analyze the inner workings of such malware.

Root kits
The detection of root kits are a major challenge for anti-virus programs. Root kits are extremely difficult to detect and if undetected, root kits have full administrative access to the computer and are invisible to users, so that they will not be shown in the list of running processes in the task. Root kits can modify the inner workings of the operating system and tamper with antivirus programs.

Damaged files
Files which have been damaged by computer viruses are normally damaged beyond recovery. Anti-virus software removes the virus code from the file during disinfection, but this does not always restore the file to its undamaged state. In such circumstances, damaged files can only be restored from existing backups.

Installed antivirus software running on an individual computer is only one method of guarding against viruses. Other methods are also used, including cloud-based antivirus, firewalls and on-line scanners.

Cloud antivirus
Cloud antivirus is a technology that uses lightweight agent software on the protected computer, while offloading the majority of data analysis to the provider's infrastructure.

One approach to implementing cloud antivirus involves scanning suspicious files using multiple antivirus engines. This approach was proposed by an early implementation of the cloud antivirus concept called CloudAV. CloudAV was designed to send programs or documents to a network cloud where multiple antivirus and behavioral detection programs are used simultaneously in order to improve detection rates. Parallel scanning of files using potentially incompatible antivirus scanners is achieved by spawning a virtual machine per detection engine and therefore eliminating any possible issues. CloudAV can also perform "retrospective detection," whereby the cloud detection engine rescans all files in its file access history when a new threat is identified thus improving new threat detection speed. Finally, CloudAV is a solution for effective virus scanning on devices that lack the computing power to perform the scans themselves

Network firewall
Network firewalls prevent unknown programs and processes from accessing the system. However, they are not antivirus systems and make no attempt to identify or remove anything. They may protect against infection from outside the protected computer or network, and limit the activity of any malicious software which is present by blocking incoming or outgoing requests on certain TCP/IP ports. A firewall is designed to deal with broader system threats that come from network connections into the system and is not an alternative to a virus protection system.

Online scanning
Some antivirus vendors maintain websites with free online scanning capability of the entire computer, critical areas only, local disks, folders or files.

Trojan horse
A Trojan horse, or Trojan, is software that appears to perform a desirable function for the user prior to run or install, but (perhaps in addition to the expected function) steals information or harms the system. The term is derived from the Trojan Horse story in Greek mythology.

Adware
A destructive program that masquerades as a benign application. Unlike viruses, Trojan horses do not replicate themselves but they can be just as destructive. One of the most insidious types of Trojan horse is a program that claims to rid a computer of viruses but instead introduces viruses onto the computer.
The term comes from the Greek story of the Trojan War, in which the Greeks give a giant wooden horse to their foes, the Trojans, ostensibly as a peace offering. But after the Trojans drag the horse inside their city walls, Greek soldiers sneak out of the horse's hollow belly and open the city gates, allowing their compatriots to pour in and capture Troy.

Phishing
Phishing is a way of attempting to acquire sensitive information such as usernames,passwords and credit card details by masquerading as a trustworthy entity in anelectronic communication. Communications purporting to be from popular social web sites, auction sites, online payment processors or IT administrators are commonly used to lure the unsuspecting public. Phishing is typically carried out by e-mail orinstant messaging, and it often directs users to enter details at a fake website whose look and feel are almost identical to the legitimate one. Phishing is an example of social engineering techniques used to fool users, and exploits the poor usability of current web security technologies. Attempts to deal with the growing number of reported phishing incidents include legislation, user training, public awareness, and technical security measures.