A specimen of zirconolite, collected from the type locality of the mineral originally described as zirkelite at Jacupiranga, São Paulo, Brazil has been re-examined and its mineral chemistry more completely characterized. All crystals studied are metamict and display very fine lamellar oscillatory zoning (1–3 µm in width) superimposed on a sector zonation. Such zoning, observed in backscattered electron images, is primarily related to differences in the concentration of Th.

In comparison with other reported zirconolite samples from a variety of geological occurrences, Jacupiranga zirconolite has higher Ca, Th, (Nb + Ta) and lower Ti and REE, which is consistent with its occurrence in carbonatitic rocks. The compositional variation with respect to an ideal zirconolite is described by two main coupled substitutions:

(Th,U)⁴⁺ + (Fe,Mg)²⁺ ⇌ Ca²⁺ + Ti⁴⁺, and (Th,U)⁴⁺ + (REE)³⁺ + (Nb,Ta)⁵⁺ + (Fe,Mg)²⁺ ⇌ (Ca)²⁺ + 3(Ti)⁴⁺.

Calzirtite, Ca₂Zr₅Ti₂O₁₆, although intergrown with zirconolite and with identical major components, shows much less compositional variability with only minor amounts of Nb and Ta substituting for Ti. Unlike zirconolite, the REE and actinide elements are not easily accommodated in the calzirtite structure.