It is expected that information on the source, reaction pathway, and reaction kinetics of an organic compound can be obtained from its position-specific isotope compositions or intramolecular isotope distribution (Intra-ID). To retrieve the information, we could use its predicted equilibrium Intra-ID as a reference for understanding the observed Intra-IDs. Historically, observed, apparently close-to-equilibrium carbon Intra-ID has prompted an open debate on the nature of biosystems and specifically the pervasiveness of reversible biochemical reactions. Much of the debate remains unresolved, and the discussion has not clearly distinguished between two states of equilibrium: (1) the equilibrium among the corresponding bond-breaking and bond-forming positions in reactant and product and (2) the equilibrium among all carbon positions within a compound. For an organic molecule with multiple carbon positions, equilibrium carbon Intra-ID can be attained only when a specific reaction is in equilibrium and the sources of each position are also in equilibrium with each other. An observed Intra-ID provides limited information on if the sources and pathways are both unconstrained. Here, we elaborate on this insight using examples of the observed Intra-IDs of hydroxyl-bearing minerals, N2O, and acetic acid. Research effort aiming to calibrate position-specific equilibrium and kinetic isotope fractionation factors for defined processes will help to interpret observed Intra-IDs of a compound accurately and fully.