Initially used as antimalarial drugs, hydroxychloroquine (
HCQ
) and, to a lesser extent, chloroquine (
CQ
) are currently being used to treat several diseases. Due to its cost‐effectiveness, safety and efficacy,
HCQ
is especially used in rheumatic autoimmune disorders (
RAD
s), such as systemic lupus erythematosus, primary Sjögren's syndrome and rheumatoid arthritis. Despite this widespread use in the clinic,
HCQ
molecular modes of action are still not completely understood. By influencing several cellular pathways through different mechanisms,
CQ
and
HCQ
inhibit multiple endolysosomal functions, including autophagy, as well as endosomal Toll‐like receptor activation and calcium signalling. These effects alter several aspects of the immune system with the synergistic consequence of reducing pro‐inflammatory cytokine production and release, one of the most marked symptoms of
RAD
s. Here, we review the current knowledge on the molecular modes of action of these drugs and the circumstances under which they trigger side effects. This is of particular importance as the therapeutic use of
HCQ
is expanding beyond the treatment of malaria and
RAD
s.