Transcriptome studies are essential to understanding the complexity of the genetic regulation of both disease and health. However, the short-read sequencing platforms such as Illumina RNA-Seq cannot reliably differentiate between transcript isoforms created by alternate splicing of pre-mRNA. The Pacific Biosciences (PacBio) RS II platform with Iso-Seq protocol can read long stretches of sequences and, therefore, reliably distinguish between transcript isoforms of the same gene. In this study, glomerular and tubulointerstitial compartments microdissected from healthy human kidney tissue in tumor nephrectomy samples were sequenced with the PacBio RS II platform. These transcripts were then validated using transcripts of the same samples by the traditional Illumina RNA-Seq protocol, distinct Illumina RNA-Seq short reads from European Renal cDNA Bank (ERCB) samples, and annotated GENCODE transcript list, thus identifying novel transcripts. We identified 14,739 and 14,259 annotated transcripts, and 17,268 and 13,118 potentially novel transcripts in the glomerular and tubulointerstitial compartments, respectively.