Because of increasing concern about widespread use of insecticides and fungicides, we have developed a highly sensitive analytical method to quantify urine-specific urinary biomarkers of the organophosphorus pesticides acephate, methamidophos, omethoate, dimethoate, and two metabolites from the fungicides alkylenebis-(dithiocarbamate) family: ethylenethiourea and propylenethiourea. The general sample preparation included lyophilization of the urine samples followed by extraction with dichloromethane. The analytical separation was performed by high-performance liquid chromatography (HPLC), and detection by a triple quadrupole mass spectrometer with and atmospheric pressure chemical ionization source in positive ion mode using multiple reaction monitoring and tandem mass spectrometry (MS/MS) analysis. Two different Thermo-Finnigan (San Jose, CA, USA) triple quadrupole mass spectrometers, a TSQ 7,000 and a TSQ Quantum Ultra, were used in these analyses; results are presented comparing the method specifications of these two instruments. Isotopically labeled internal standards were used for three of the analytes. The use of labeled internal standards in combination with HPLC-MS/MS provided a high degree of selectivity and precision. Repeated analysis of urine samples spiked with high, medium and low concentration of the analytes gave relative standard deviations of less than 18%. For all compounds the extraction efficiency ranged between 52% and 63%, relative recoveries were about 100%, and the limits of detection were in the range of 0.001-0.282 ng/ml.