In parasitological examination of stool, permanent staining methods are preferred because they enable stool preparations be examined afterwards and they define internal structures of protozoons, besides showing higher sensitivity compared to native-lugol examination. Trichrome staining method is frequently used as permanent staining method. Conventional trichrome staining is multiple-stage, preparation and application is troublesome, but there are commercial trichrome products prepared in a short time, having fewer stages and solutions of which are brought into use in kit. This study is carried out for comparing conventional and commercial trichrome staining methods in detection of protozoan in the stool. 155 stool samples sent for parasitical examination are stained with conventional and commercial (PARAPAK (R), ECOSTAIN, Meridian Bioscience, Inc, USA) trichrome stain and examined microbiologically; both methods are evaluated in terms of staining quality based on detection of protozoons, the number of protozoons detected in each area and having typical morphological features of protozoons. The difference between conventional and commercial methods in detection of protozoan is not statistically significant (P=0.752). Besides, the sensitivity of commercial trichrome staining method is 78.2% compared to conventional method, specificity is 99.2%. Although no statistically significant differences are detected between two methods as to number of parasites in each area (P=0.545), when they are compared with respect to having morphological features of protozoons, statistically significant difference is detected (P=0.008).