Aims of this study were to provide firsthand data on the incidence of trace metals in human seminal plasma and find possible correlations between levels of toxic metals and semen quality of Pakistani population. Human semen samples were collected from male partners of couples undergoing infertility assessment at the National Institute of Health Islamabad (Pakistan). We investigated seventy-five seminal plasma samples, which were further categorized into three groups (normozoospermia, oligozoospermia and azoospermia) according to WHO guidelines. The concentration of 17 different toxic metals in human seminal plasma was determined simultaneously by using Inductively coupled plasma mass spectrometry (ICP-MS). Out of 17 trace metals, Cd and Ni showed significant difference (p < 0.05) among three monitored groups. Ni and Cd concentrations in the seminal plasma were negatively correlated with sperm concentration (r = -0.26, -0.29) and motility (r = -0.33, -0.37), respectively. This study suggested that exposure of Ni and Cd is mainly related with the consumption of contaminated dietary items, including ghee (cooking oil), flour and other agri-products. In some semen samples, the concentrations of Sn, V, Cu, Pb, Cr and Hg exhibited high levels suggesting a recent human exposure to surrounding sources. In Pakistani human semen samples, the levels of trace metals were lower and/or comparable to that found in populations of other countries. The results show the first evidence of the effect of toxic metals on semen quality and male infertility in Pakistan.