This paper presents results from positive matrix factorization (PMF) of organic molecular marker data to investigate the sources of organic carbon (OC) in Pittsburgh, Pennsylvania. PMF analysis of 21 different combinations of input species found essentially the same seven factors with distinctive source-class-specific groupings of molecular markers. To link factors with source classes we directly compare PMF factor profiles with actual source profiles. Six of the PMF factors appear related to primary emissions from sources such as motor vehicles, biomass combustion, and food cooking. Each primary factor contributed between 5% and 10% of the annual-average OC with the exception of the cooking related factor which contributed 20% of the OC. However, the contribution of the cooking factor was sensitive to the specific combinations of input species. PMF could not differentiate between gasoline and diesel emissions, but the aggregate contribution of primary emissions from these two source classes is estimated to be less than 10% of the annual-average OC. One factor appears related to secondary organic aerosol based on its substantial contribution to biogenic oxidation products. This secondary factor contributed more than 50% of the summertime average OC. Reasonable agreement was observed between the PMF results and those of a previously published chemical mass balance (CMB) analysis of the same molecular marker dataset. Individual PMF factors are correlated with specific CMB sources, but systematic biases exist between the two estimates. These biases were generally within the uncertainty of the two estimates, but there is also evidence that PMF is not cleanly differentiating between source classes.