Background: Iron deficiency anemia (IDA) during pregnancy is a common nutritional disorder with adverse effects for the baby, such as premature birth and low birth weight, and the mother, such as cardiovascular symptoms and reduced physical and mental strength. Therefore, identifying factors affective on IDA will assist the improvement of the health of the mother and fetus. This study aimed to determine the prevalence of IDA in the first and third trimester of pregnancy and some related factors in pregnant women referred to healthcare centers in Bandar Lengeh, Iran, in 2015. Materials and Methods: In this cross-sectional study, 418 pregnant women, who were referred to health centers in the city and had completed their pregnancy, were assessed through systematic sampling. Data were collected using the researcher-made checklist and through a review of health records. Data were analyzed using chi-square, Fisher's exact, and McNemar's test. Results: The mean age of the participants was 27.17 ± 5.62 and most participants were in the age group of 18-35, had high school education, were homemakers, and experienced their first pregnancy. The findings of the study showed that the prevalence of IDA was 22.5% (confidence interval: 18.4%-26.5%) and 45.9% (Confidence interval: 41.1%-50.6%) in first and third trimester of pregnancy, respectively. IDA in first and third trimester of pregnancy had significant correlation with pregnancy interval (P < 0.009 and P < 0.001, respectively); with increase in the pregnancy interval, the prevalence of IDA also increased. Conclusions: According to the results, it seems that the prevalence of IDA was undesirable, especially in the third trimester. Since this eating disorder is a preventable complication and pregnant women are a group at risk of anemia, attention to the expansion of pre-pregnancy care, increased awareness of mothers regarding appropriate nutrition and maintenance of a diverse and balanced diet, regular consumption of supplements, contraception in older women, and maintenance of appropriate intervals between pregnancies seem essential.