Acute rheumatic fever (ARF) is a serious post-infectious condition that can develop after a Streptococcus A (StrepA) infection, which can result in permanent heart valve damage and rheumatic heart disease. The rates of ARF in Indigenous children in New Zealand and Australia are amongst the highest globally but disease mechanisms are poorly understood. The current hypothesis is based on molecular mimicry generating antibodies in response to StrepA infection, which cross-react with cardiac proteins such as myosin. Contemporary investigations of the broader autoantibody response in ARF are needed to both inform pathogenesis models and identify new biomarkers for the disease. In prior work we utilised high content protein arrays (Protoarray, 9000 proteins and HuProt Array, 16,000 proteins) to analyse ARF sera autoreactivity and showed broad yet heterogenous elevation of autoantibodies. To enable deeper exploration of ARF autoantibodies this study employed Phage Immunoprecipitation Sequencing (PhIP-seq) and a human autoantigen library comprised 259,345 overlapping 90-mer peptide sequences covering the human proteome. Sera from 52 ARF cases and 75 matched controls from the national Rheumatic Fever Risk Factor study were incubated with the library and next-generation sequencing of enriched clones was performed. PhIP-seq data was analysed using both conventional differential expression analysis, as well as more robust multivariate dimensionality reduction techniques in order to generate robust results. Both analyses confirmed a global increase in autoantigen reactivity in ARF patients compared with controls, as well as marked heterogeneity in the autoantibody fingerprint between ARF patients. This heterogeneity was reflected in the large proportion of private autoantibodies identified, with public autoantibodies (common between individuals) comprising just 1% of the enriched peptides. Filtering for peptides that were identified in both types of analysis, and were considered 'public', resulted in the identification of both historic and novel autoantigens with roles in heart structure and function. Orthogonal validation in optimised immunoassays indicates multiple autoantigens will need to be combined to capture the heterogeneity observed in future diagnostic tests.