We present a method to calculate Lyapunov exponents of rigid diatomic molecules in three dimensions (12N-dimensional phase space). The spectra of Lyapunov exponents are obtained for 32 rigid diatomic molecules interacting through the Weeks-Chandler-Anderson potential for various bond length and densities, and compared with those of Shin et al. [Phys. Rev. E 64, 041106 (2001)]. Our algorithm is easy to implement and total CPU time is relatively inexpensive.