Acyl-CoA hydrolase activity was studied in brown adipose tissue (BAT) mitochondria of rats. The substrate specificity was investigated: total hydrolase activity showed two activity peaks, one sharp peak for propionyl-CoA and a broad peak at medium- to long-chain acyl-CoAs. The propionyl-CoA activity fully comigrated with a mitochondrial matrix marker enzyme in fractionation studies of tissue and mitochondria. The hydrolytic activity against short-chain acyl-CoAs was inhibited by NADH, and analyses of the substrate specificity of the hydrolases in the presence and absence of NADH allowed for the delineation of two distinct acyl-CoA hydrolases. These hydrolases could also be separated by gel filtration. It was concluded that rat BAT mitochondria possess at least two matrix acyl-CoA hydrolases: one broad-spectrum acyl-CoA hydrolase with an apparent native molecular weight of less than 100,000, and a specific propionyl-CoA hydrolase with an apparent native molecular weight at least 240,000; this hydrolase is regulated by NADH. It is suggested that the function of the propionyl-CoA hydrolase is to ensure that the level of propionyl-CoA in the mitochondria is not detrimentally increased.