Background: Polycystic ovarian syndrome (PCOS) is the most common cause of anovulatory infertility. Hyperhomocysteinemia (HHcy), is common in PCOS and reportedly causes poor oocyte quality and recurrent pregnancy loss. The aim of this report is to assess serum concentrations of Hcy and its association with C-reactive protein (CRP) levels in patients with PCOS undergoing in-vitro fertilization (IVF) treatment. Materials and Methods: Eighty-five women of reproductive age 25–35 years were included in this study, comprising 30 infertile women with PCOS (group 1), 30 infertile women without PCOS (group 2), and 25 matched apparently healthy women without infertility or PCOS (group 3). The serum Hcy and CRP levels were measured using the TOSOH AIA 360 enzyme immunoassay method and Raytor6000 Semi-Autoanalyzer, respectively. Results: The median CRP values were 15.13 (4.43–21.77 mg/L), 3.42 (2.50–8.04 mg/L), and 1.45 (0.97–3.51 mg/L) for Group 1, Group 2, and Group 3, respectively. The median Hcy values were 19.75 (15.50–39.98 μmol/L), 10.00 (9.38–10.92 μmol/L), and 10.00 (8.93–10.93 μmol/L) for Group 1, Group 2, and Group 3, respectively. The differences between Group 1 and Group 2, and between Group 1 and Group 3 median Hcy values were significant for both CPR and Hcy (P < 0.0001). There was a significant association between embryo qualities and the groups. Similarly, there were more of higher (Grades 4 and 5) embryo qualities in Group 3. Conclusion: Serum Hcy and CRP levels estimation should be included in the evaluation and management of patients with PCOS undergoing in-vitro fertilization.