***Sequenced placenta, serum and urine miRNomes of three healthy pregnancies*** Authors: R. Inno, M. Laan Chair of Human Genetics, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu 50411, Estonia Corresponding author: M. Laan email: maris.laan@ut.ee ***General information*** This dataset contains microRNA sequencing data form three healthy pregnant females. Expression values of placenta, serum and urine samples are given in CPM (count per million). ***Methodology*** RNA was extracted using Qiagen miRNeasy Mini kit (Qiagen, Hilden, Germany). Library preparation (QIAseq® miRNA Library Kit) and single-end sequencing (75 bp read length) were conducted at the laboratory of the service provider (Qiagen, Hilden, Germany). MicroRNA sequencing was carried out on the Illumina NextSeq500 platform (San Diego, CA, USA). The basic bioinformatic workflow was carried out by Qiagen Genomic Service implemented on CLC Genomics Server (version 20.0)(Qiagen, Aarhus, Denmark). ***Description of the data in the data set*** Data is organized by microRNA names for all used samples. Median values for a tissue type is shown after individual values. Data specific information: CPM, counts per million; Ind, individual ***Sharing and Access information*** This data is made public for other researchers to use in their own work under CC BY.