Introduction: Modular diets (MDs) with low amount of offending amino acids have been developed using locally available food ingredients as alternatives to commercial formulas for the treatment of branched-chain organic acidurias (BCOAs). Herein, we conducted a clinical investigation of MDs in patients with BCOAs. Methods: Modular diet A (MDA), with low leucine was produced for maple syrup urine disease (MSUD), and modular diet B (MDB) products, MDB-1, -2, -3, and -4, with low leucine, valine, methionine and threonine were made for isovaleric aciduria (IVA)/methylmalonic aciduria (MMA)/propionic aciduria (PA). Children aged 4-18 years, with MSUD, IVA, PA or MMA were invited to participate in the study. The research subjects switched from metabolic formula protocol to modular diet protocol. They were followed-up at 0, 1, 2, 4, and 6 months. Clinical efficacies of MDs were determined by completion of study, compliance to MDs, clinical outcomes and complications, and parental satisfaction. Results: Six children (2 MSUD and 4 IVA) participated and completed the study. Compliance to MDA was 100% in MSUD subjects with G-tube feeding, while compliance to MDB varied among self-fed individuals with IVA. One subject with MSUD was clinically stable throughout the study, while the other experienced metabolic instability. All IVA individuals showed clinical and laboratory stability during the study. One MSUD and three IVA families preferred the metabolic formula, whereas the other IVA family reported no preference and the other MSUD subject preferred MDs. Conclusion: We provided a proof of concept in developing modular diets for BCOAs, and showed favourable outcomes when using MDs in IVA and varying clinical benefits in MSUD.