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Background:The microbial colonization of the neonates gastrointestinal tract is an essential process in the human lifecycle and have important consequences for human health and disease. However, information about composition of meconium microbiota in neonates with clinical problem is lacking in Indonesian populations. Objective:This study aimed to obtain preliminary profile of meconium microbiota in neonates with some clinical outcomes in Indonesian population. Materials and Methods:We enrolled 15 neonates providing meconium samples from February to March 2019 and treated in the National Referral Hospital Cipto Mangunkusumo, Jakarta, Indonesia. Subjects’ characteristics, such as feeding pattern, birth weight, delivery mode, and breathing assistance were obtained from medical records. Each sample was cultured microbiologically on selective and nonselective media to quantify cultivable bacteria and allow further study of the isolate. Identification based on selective media, morphology, microscopy, and molecular technique by Polymerase Chain Reaction-16s rRNA sequencing were performed to provide deeper information about bacterial diversity prior to profile the meconium microbiota. Meconium microbiota profile and the clinical outcomes comprising neonatal necrotizing enterocolitis (NEC), sepsis, and hyperbilirubinemia were analyzed. Results:Aside from hyperbilirubinemia, we didn’t discover other clinical outcomes such as neonatal sepsis and NEC. Staphylococcus, particularly Staphylococcus hominis, andBacilluswere detected as dominant bacteria in neonates’ meconium, followed by Streptococcus,Enterococcus, and Enterobacter. Enterobacter hormaechei, Enterococcus faecalis, Erwinia billingae, Klebsiella pneumoniae, Micrococcus luteus, andAtlantibacter hermannii were found only in hyperbilirubinemia neonates whileEnterococcus hirae, Acinetobacter baumannii, Brevibacillus agri, andPseudomonas stutzeri were found only in neonates without hyperbilirubinemia. Conclusion:We didn’t find other clinical outcomes except hyperbilirubinemia in this study. Profile of meconium microbiota in neonates with and without hyperbilirubinemia was predominated by Staphylococcusand Bacilluswith the difference in the species and abundance and also consists of unique species and low abundance bacteria in each profile.