The significance of islet antigen-reactive T cells found in peripheral blood of type 1 diabetes (T1D) subjects is unclear, partly because similar cells are also found in healthy control (HC) subjects. We hypothesized that key disease-associated cells would show evidence of prior antigen exposure, inferred from expanded T cell receptor (TCR) clonotypes, and essential phenotypic properties in their transcriptomes. To test this, we developed single-cell RNA sequencing (RNA-seq) procedures for identifying TCR clonotypes and transcript phenotypes in individual T cells. We applied these procedures to analysis of islet- antigen reactive CD4+ memory T cells from the blood of T1D and HC individuals following activation with pooled immunodominant islet peptides. We found extensive TCR clonotype sharing in antigen-activated cells, especially from individual T1D subjects, consistent with in vivo T cell expansion during disease progression. The expanded clonotype from one T1D subject was detected at repeat visits spanning more than 15 months, demonstrating clonotype stability. Notably, we found no clonotype sharing between subjects, indicating a predominance of “private” TCR specificities. Expanded clones from two T1D subjects recognized distinct IGRP peptides, implicating this molecule as a trigger for CD4+ T cell expansion. While overall transcript profiles of cells from HC and T1D subjects were similar, profiles from the most expanded clones were distinctive. Our findings demonstrate that islet- antigen reactive CD4+ memory T cells with unique antigen specificities and phenotypes are expanded during disease progression and can be detected by single-cell analysis of peripheral blood.