Single cell analysis has numerous potential applications, for instance in the context of myotonic dystrophy type I (DM1). This disease is caused by a CTG expansion in the dystrophia myotonica-protein kinase (DMPK) gene, with CTG expansion length being heterogeneous not only between tissues but also between cells in the same tissue. We studied muscle pathophysiology from five patients with DM1 at single cell level, including RNA foci (i.e., nuclear DMPK-transcribed aggregates that trap proteins) and splicing alterations (caused by trapping of important splicing regulator proteins by the RNA foci). Single cell myoblasts were heterogeneous in RNA foci load, with most showing 0 to 3 foci. The percentage of myoblasts carrying foci differed among patients, ranging from 29 to 99%. We found a significant direct correlation between mean and median number of RNA foci in myoblasts and patients’ endurance capacity (r=-0.975, p=0.005). Although the expression of DMPK and MBNL1 transcripts was variable among the myoblasts, no relationship was found between RNA foci number and their expression in individual cells. CTG size in muscle correlated with patients´ disease onset. In summary, single cell analysis poses some technical challenges but allows an in-depth analysis of heterogeneous molecular alterations in patients with DM1.