Serum and plasma are two of the most commonly used materials in clinical diagnosis and investigations. Whether differential nucleic acids exist between the serum and plasma, and the way in which they may be selected in clinical diagnosis and applications remains to be elucidated. The present study sequenced microRNAs (miRNAs) in the serum and plasma of pregnant females using next generation sequencing technology. Several differentially expressed miRNAs were also verified by reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR). In total, 329 miRNAs and 193 miRNAs were detected in maternal serum and plasma. Differential expression and different types of miRNAs were found in the serum and plasma, among them, 19 were upregulated and 6 were downregulated in serum when compared with plasma with a fold change >2.0 (P<0.001). The results demonstrated that a number of miRNAs were differentially expressed in the serum and plasma, and several of the miRNAs expressed in the serum were absent in the plasma. The results obtained using RT‑qPCR in the selected miRNAs were similar to these results, and indicated that the differential expression of miRNAs in the serum and plasma provide a guide for further investigation and clinical use. The results of the analysis also suggested that differentially expressed DNA and RNA in the serum and plasma of pregnant females may be a result of the differential expression of miRNAs.