Background: Pregnancy is a critical period where optimal maternal and fetal health depends on adequate nutritional status. Deficiencies in essential vitamins, such as vitamin D, vitamin B12, and folate, can result in adverse health outcomes. Objective: This study aims to assess the serum levels of vitamin D, vitamin B12, and folate in early pregnancy. Methodology: This cross-sectional research was conducted at Kurdistan Private Hospital in Duhok, Kurdistan Region of Iraq, from September 2022 to October 2023. The study included 150 pregnant women, with ages ranging from 18 to 45 years. Serum levels of vitamin D, vitamin B12, and folate were measured using the Automatic Clinical Chemistry Analyzer COBAS e 411 (Roche Diagnostics, Basel, Switzerland). Results: The mean age of the participants was 29 years (standard deviation [SD] = 6.2 years), with ages ranging from 18 to 45 years. The average serum human chorionic gonadotropin (HCG) level was 4,292 mIU/mL (SD = 3,947 mIU/mL), with a range of 98 to 10,000 mIU/mL. The mean serum levels were 17.8 ng/mL (SD = 11.6) for vitamin D, 367 pg/mL (SD = 245) for vitamin B12, and 11.5 ng/mL (SD = 4.6) for folate. The prevalence of vitamin D deficiency was significant, with 92 participants (61.3%) having levels below 20 ng/mL, 39 participants (26%) having insufficient levels ranging from 20 to 29 ng/mL, and only 19 participants (12.7%) having sufficient levels between 30 and 100 ng/mL. No cases of vitamin D toxicity (>150 ng/mL) were observed. Regarding vitamin B12, 32 participants (21.3%) had deficient levels (<200 pg/mL), while 118 participants (78.7%) had normal levels. Folate analysis revealed that 3 participants (2%) had moderate deficiency (2-3 ng/mL), 14 participants (9.3%) had mild deficiency (3-6 ng/mL), and there were no cases of severe folate deficiency (<2 ng/mL). Pearson correlation analysis showed weak correlations between the study variables, with the strongest being a weak negative correlation between age and serum folate levels (-0.18). Conclusions: The study found a high prevalence of vitamin D deficiency among the pregnant women included in the study, while the levels of folate and vitamin B12 were comparable to worldwide estimates. These findings focus attention on the importance of monitoring and addressing nutritional deficiencies at the beginning and throughout pregnancy. They also underline the need for preventive health interventions to correct these deficiencies and achieve the best outcomes for both maternal and fetal health.