Objective To present and validate a multifunctional electronic medical record (EMR) for outpatient care to women with endocrine disorders in pregnancy and to compare health information data fill rate to conventional medical records. Methods We developed an EMR named Ambulatory of Endocrine Diseases in Pregnancy (AMBEG) for systematic registration of health information The AMBEG was used for obstetric and endocrine care in a sample of pregnant women admitted to the maternity reference in high-risk pregnancies in Bahia from January 2010 to December 2013. We randomly selected 100 patients accompanied with AMBEG and 100 patients monitored with conventional consultation and compared the health information data fill rate of the electronic consultation to that performed using conventional medical records. Results 1461 consultations were held, of which 253, 963 and 245 were first, follow-up and puerperium consultations, respectively. Most patients were pregnant women with diabetes (77.2%) and 60.1% were women with pre-gestational diabetes. The AMBEG satisfactorily replaced the conventional medical record. The percentage of registered information was significantly higher in the AMBEG: clinical symptoms (87% versus 100, p < 0.01), uterine height (89 versus 75%, p = 0.01), total weight gain (91 versus 40%, p < 0.01) and specific diabetes data (diet, insulin regimen, glycemic control and management of hypoglycemia) revealed a significant difference ( p < 0.01). The ability to export data to worksheets greatly facilitated and accelerated the statistical analysis of the data. Conclusions AMBEG is a useful tool in clinical care for women with endocrine diseases during pregnancy. The fill rate of clinical information was superior to that registered in conventional medical records.