Introduction Israel has absorbed >40,000 Eritrean undocumented migrants since 2007, while the majority live in the southern neighborhoods of Tel-Aviv. As non-citizens and citizens infants in Israel receive free preventive treatment at the mother and child health clinics (MCHC), this study aimed to compare development and growth achievements between children of Eritrean mothers (CE) to children of Israeli mothers (CI), and assess their compliance to routine follow-up and vaccination-timeliness. Methods This cohort study included all Israeli-born CE between 2009 and 2011, compared with a random sample of CI and treated at the same MCHC and followed-up to the age of 30-months. Dependent outcomes included anthropometric measurements, developmental achievements and adherence to immunization schedule. Results Of all 271 CE who were compared with 293 CI, no statistically significant differences were found in birth anthropometric measurements. Yet, CE had increased weight and length than CI after reaching one year of age (p<0.05). CE were more likely to fail in tests assessing fine-motor skills, linguistic and socio-emotional domains than CI, while no statistical difference was found in gross-motor achievements. At the end of follow-up, 203 (74.9%) of the CE and 271 (74.1%) of the CI completed the vaccination schedule, p = 0.9. Conclusion CE had greater anthropometric measurements than CI after one year of age, and showed higher impairments in fine motor, linguistic and socio-emotional domains. Adherence to vaccination was similar. The inequalities in child health should be responded in the MCTC, and Eritrean mothers should be trained with the current recommendations for child well-being.