[3] His early work focussed on the biology, systematics and anatomy of insects, especially termites, as in Studien über südamerikanische Termiten (1906) and Termitenstudien (1909–1912).

In later work he focused on the structure of the brain in worms, arthropods and vertebrates, publishing Vergleichende Anatomie des Gehirns (1916) (Comparative anatomy of the brain), Zur Anatomie des Gehirns von Myxine (1919), Zur Anatomie und Histologie des Vorder- und Zwischenhirns der Knochenfiske (1920), Points of view concerning forebrain morphology in lower vertebrates (1922), (with C. J. van der Horst) Contribution to the morphology of the brain in Ceratodus (1925), and Points of view concerning forebrain morphology in higher vertebrates (1925).

This work made him a world expert on the nervous systems of the lower vertebrates.

Holmgren, who undertook a research trip to Bolivia and Peru in 1904–1905, was from 1920 the publisher of the journal Acta Zoologica.

[4] Holmgren was elected a member of the Royal Swedish Academy of Sciences in 1928.