Among the possible risk factors for male reproduction, exposure to phthalates and alkylphenols is widely documented. This study evaluated the possible association between chemical exposure and the quality of the seminal fluid of 105 subjects in a fertility clinic. The urinary levels of seven phthalate metabolites (monoethylphthalate, MEP; monobenzylphthalate, MBzP; mono n-butylphthalate, MnBP; mono-(2-ethylhexyl) phthalate, MEHP; mono(2-ethyl-5-hydroxyhexyl) phthalate, MEHHP; mono-n-octylphthalate, MnOP; mono-isononylphthalate, MiNP) and bisphenol A (BPA), were analysed by high performance liquid chromatography/tandem mass spectrometry HPLC/MS/MS. The regression analysis showed that the semen volume was positively associated with MnBP, MnOP and BPA levels while was negatively associated with MiNP levels. The sperm concentration had a significant inverse relationship with MEP levels. A negative association was found between the use of plastic containers for food storage (p = 0.037) and semen volume (3.06 vs. 2.30 mL as average values, never vs daily). A significant positive correlation emerged (p < 0.005) between the consumption of canned food and the levels of BPA (2.81 vs. 0.14 µg/g creat as average values, daily vs. never) and between the use of perfumes and levels of MEP (389.86 vs. 48.68 µg/g creat, as average values, daily vs. never). No further statistically significant associations were found, even considering the working activity. Some evidence emerged about the possible link between exposure and seminal fluid quality: further case/control or prospective studies will allow us to confirm this causality hypothesis.