Like all plant life, cannabis can be a breeding ground for molds, fungi, bacteria, and other microbes. Under certain conditions, an unwanted ecosystem may spring forth. Indoor growing environments tend to be more prone to mold, as there is an abundance of heat and moisture indoors, and an absence of harsh conditions that exists in an outdoor environment. Many of these organisms produce toxins that are harmful to human health.

Mycotoxins are harmful compounds that are created by certain molds. These toxins may exist on cannabis crops, and need to be screened for. Many mycotoxins, including aflatoxins can persist throughout the processing steps, and can cause disease and cancers for the end user. For patients using medical marijuana, their often-weakened immune systems leave them vulnerable to such harmful compounds. HPLC or LC-MS systems are often used for mycotoxin analysis.