Purpose Microbiota has crucial biological importance for human well-being. Bidirectional interaction exists between microbiota and the host, and there have been no studies investigating this interaction in patients with acromegaly. We aimed to analyze the composition of microbiota in patients with newly diagnosed acromegaly. Method Stool samples were obtained from the patients with newly diagnosed acromegaly in the Endocrinology Clinic of Erciyes University Medical School. The composition of microbiota was analyzed, and the results were compared to healthy volunteers matched to the patients in terms of age, gender and body mass index. Results Seven patients (three male, four female) with a mean age of 48 +/- 17.6 years were included in the study. The stool analysis revealed a significantly lower bacterial diversity in the patients with acromegaly. Bacteroidetes phylum was predominating in the patient group, and Firmicutes/Bacteroidetes ratio was altered significantly. Bifidobacterium, Collinsella, Bacteroides, Butyricimonas, Clostridium, Oscillospira, and Dialister were predominating in the control group. Conclusion The gut microbiota is significantly altered in patients with newly diagnosed acromegaly. Further prospective studies are needed to elucidate the causative relationship between acromegaly, colorectal pathologies, and microbial alterations.