Notable progress has been made in methods that encourage the use of PCR as a rapid and accurate tool in quality evaluation of pharmaceuticals. In this study, monoplex and multiplex PCR based assays were developed and compared with standard conventional methods for rapid detection of three specified topical indicator pathogens, Pseudomonas aeruginosa, Staphylococcus aureus and Candida albicans, in nonsterile pharmaceutical preparations. The detection limit of monoplex PCR assays for the microbial targets was achieved at 100 fg purified DNA and 10 CFU/ml for Pseudomonas aeruginosa and 1fg purified DNA and 10 CFU/ml for each of Staphylococcus aureus and Candida albicans. No change in the detection limit for cfu/ml of the three tested indicator pathogens was obtained upon using mPCR assays. The results of applying both conventional and PCR detection methods for different cream and lotion preparations revealed a 100% correlation between both methods. The PCR based detection method can be completed in 8 h versus 5-6 days in case of conventional methods, but the former can't differentiate between viable and dead cells. PCR assays can be used efficiently and in a cost-effective manner to exclude the contamination of pharmaceutical products by the indicator pathogens. Even though in case of contamination by non-viable indicator organism, PCR technique can still be used after partial incubation of cultivated test sample. Thus, PCR assays provide specific, reliable results that can be incorporated in quality evaluation of pharmaceuticals and will impact positively in terms of cost and time.