In Huntington’s disease (HD), symptoms occur late in life. However, an earlier neurodevelopmental and pre-manifest period exists in juvenile and ultra-juvenile HD (and other neuro-diseases). In order to deliver the missing knowledge about defective brain formation, we used juvenile HD and control iPSC and established 2-months old 3D fused brain organoids of dorsal and ventral forebrain identity. We confirmed their specification into various distinct regions such as PAX6+ ventricular zone and TBR1+ subventricular zone, NKX2.1+ and DLX2+ medial ganglionic eminence (MGE), GSX2+ lateral ganglionic eminence (LGE), and TTR+ choroid plexus. By conducting qPCR experiments, we demonstrate that the transcriptomics of several neuronal and glial markers is altered in juvenile HD organoids. Detecting early neurodevelopmental cellular phenotypes in cell composition during development in organoids that are not as specified as the human brain requires single-cell RNA-seq and a special high-resolution bioinformatics pipeline. Therefore we constructed a unique JSEQ® pipeline and performed the scRNA-seq analysis of HD71Q and HD77Q vs. control 17Q and 21Q organoids to determine early alterations in HD cells during brain formation. The JSEQ® bioinformatics pipeline performs all entry steps in single-cell sequencing analyses and subsequently determines high-resolution cell composition by the combinatorial CSSG algorithm. Combining the scRNA-seq and JSEQ pipeline, we identified several cell populations particularly vulnerable in juvenile HD. Overall, we present the formation of fused brain organoids and early transcriptomic changes in juvenile HD neurodevelopment.