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Petri dishes are often used to make agar plates for microbiology studies. The dish is partially filled with warm liquid containing agar and a mixture of specific ingredients that may include nutrients, blood, salts, carbohydrates, dyes, indicators, amino acids or antibiotics. 

Once the agar cools and solidifies, the dish is ready to be inoculated with a microbe-laden sample. Virus or phage cultures require a two-stage inoculation: after the agar preparation, bacteria are grown in the dish to provide hosts for the viral inoculum.

Petri plates are incubated upside-down to lessen the risk of contamination from airborne particles settling on them and to prevent the accumulation of any water condensation that may otherwise disturb or compromise a culture.

While Petri dishes are widespread in microbiological research, smaller dishes tend to be used for large-scale studies in which growing cells in Petri dishes can be relatively expensive and labor-intensive.

A special type of petri dishes are Replicate Organism Detection And Counting often also referred to as rodac plates or contact plates. Those are petri dishes in which the medium protrudes (raised agar level) the edges of the dish to make it easier to take samples on hard objects. The plates are also divided in squares to make counting of CFUs easier. They are often used to monitor how clean certain areas are.