MicroRNAs (miRNAs) show great promise as therapeutic agents and targets in disease treatment, and knowledge of how their profile varies between normal and hypertrophied heart tissue is crucial for a better understanding of the mechanisms governing cardiac dysfunction. A small RNA cDNA library was generated from left ventricular tissue of 8-month old male spontaneously hypertensive heart failure rats (SHHF; a model of cardiac hypertrophy, n=4) and Wistar-Furth controls (WF, n=5). miRNA expression was investigated using Illumina next-generation sequencing and CLC Genomics Workbench v4.0. Differences in expression (reads per million mapped to miRBase v20; RPMM) were observed for some miRNAs between the WF and SHHF samples. These included miR-133a, which is abundant in the heart, downregulated in cardiac hypertrophy/heart failure, and involved in myocardial remodelling. RPMM for grouped miR-133a sequences aligned to the canonical sequence in miRBase v20, allowing for up to 3 additions or deletions at either end and up to 2 mismatches, were 117,071.51±11891.51 (SHHF) and 172,213.62±7401.58 (WF; mean±SEM); Baggerley’s p value after false detection rate correction <.05. We and others have shown that much of cardiac miR-133a exists as isomiRs with a single base 5′ truncation (Δ1 5′ isomiRs) that changes the seed region and the set of predicted target genes. Downregulation of miR-133a is reported to occur in cardiac hypertrophy/heart failure, but this has not been investigated for individual miR-133a isomiRs. The total RPMM (without mismatches) was 35% lower in SHHF for all Δ1 5′ isomiRs (33695±3219 SHHF; 52002±3523 WF; p<.05; t-test); and 29% lower in SHHF for all ‘canonical-seed’ isomiRs (34521±3289 SHHF; 48780±3484 WF; p<.05; t-test). DIANA-microT v3.0 and TargetScan Custom together predict 746 target genes for canonical-seed isomiRs and 461 genes for Δ1 5′ isomiRs, with 294 of these genes common to both isomiR types. Of the 452 genes predicted to be targeted by canonical-seed isomiRs but not by Δ1 5′ isomiRs, there are 223 that are upregulated during myocardial remodelling, according to our analysis of the literature and microarray datasets in Gene Expression Omnibus. Of the 167 genes predicted to be targeted by Δ1 5′ isomiRs, but not by canonical-seed isomiRs, there are 81 that are upregulated during myocardial remodelling. These results provide evidence that miR-133a Δ1 5′ isomiRs are downregulated in cardiac hypertrophy, and are likely to make a selective contribution to myocardial remodelling.