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Episodic phenomena (epilepsy, migraine, and cardiac arrhythmias) are among the most common disorders afflicting humans. Early in his career, Ptácek began studying patients with rare Mendelian muscle disorders (periodic paralysis) and proposed these as a model of more common episodic disorders. In 1990, he began systematically characterizing genes causing familial forms of periodic paralysis. This series of landmark discoveries identified mutant ion channel genes and laid the groundwork for the field now called the "channelopathies." He proposed that all the work in channelopathies of skeletal muscle would be model for episodic disorders of heart and brain. Subsequently, his group and others have identified homologous genes that (when mutated) cause cardiac arrhythmias, epilepsy, and migraine. He has gone from describing new syndromes to cloning causative genes, to biological study in vitro and in vivo (animal models).

More recently, Ptácek led the team that characterized the first Mendelian variant in human circadian function. He and his colleague Ying-Hui Fu have gone on to clone and characterize numerous genes causing this phenotype. This work has led to novel insights into human circadian biology.

Ptácek is an HHMI Investigator, and an associate editor of The Journal of Clinical Investigation and Neurogenetics. He is a member of the American Academy of Arts and Sciences, the Institute of Medicine, and the National Academy of Science.