Signalling adapters MyD88 and MAL are key proteins involved in the Toll-like receptor (TLR) pathway triggering innate immunity response to pathogens. Recruitment of MyD88 to the TLRs is facilitated via association of the Toll/interleukin-1 receptor (TIR) domains. It was observed previously that MAL induces assembly formation into thin crystalline arrays of MyD88 TIR domain filaments1. These crystalline assemblies are too small for conventional x-ray crystallography, yet are highly suitable for structure elucidation by microcrystal electron diffraction (MicroED)2-6. Here, we used MicroED to solve the structure of the MyD88 TIR domain from the filamentous assemblies. Even though the filaments tended to adhere and bundle together, selecting only single isolated crystals with a diameter of 50-150 nm using a 1 μm diameter parallel beam enabled us to collect high-quality diffraction data. After initially failing to find a convincing solution using available structures of MyD88 TIR, the structure was solved by molecular replacement using a distantly related TIR domain homologue with only 30% sequence identity. The electrostatic potential map at 3.0 Å resolution was of sufficient quality for accurate interpretation and modelling the structure using reciprocal space methods and rebuilding via interactive molecular dynamics7. Several loop regions appeared to be remodelled compared to monomeric protein determined previously by NMR8 and single-crystal x-ray diffraction9, providing us with novel insights into the structural basis of signalling by TIR domains in TLR and interleukin-1 receptor pathways.