This document describes a process for seeking EPA approval of microbiological alternate test procedures (ATPs) or new methods for use in monitoring drinking water, ambient water, wastewater, and sewage sludge (biosolids). This document serves as a supplement to the ATP guidelines at 40 CFR 136.4, 136.5, and 141.27. This ATP protocol describes a process for conducting side-by-side method comparisons and for conducting quality control (QC) acceptance criteria-based method studies for EPA-approved reference methods with QC acceptance criteria. Additionally, in some cases the revised protocol provides applicants an opportunity to demonstrate comparability by meeting QC acceptance criteria associated with the EPA-approved reference methods for different combinations of analyte and determinative technique.