Homophily in social relations is widely documented. We know that homophily results from both individual preferences and uneven opportunities for interaction, but how these two mechanisms interact in formal organizations is not well understood. We argue that organizational structures and geography delimit opportunities for interaction, but that within the opportunity sets created by business units, job functions and offices, actors have a greater level of discretion to choose their interaction partners. Therefore, we expect to observe more homophilous interactions within these structures than across their boundaries. We test this argument using a dataset consisting of millions of e-mails exchanged among thousands of employees in a large information technology firm. We find significant interaction effects between being of the same sex and being in the same business unit or same office on dyadic communication rates, though not with same job function. In an extension, we find that men's communication patterns are consistent with this theory, but that women communicate differently: relative to male-male and male-female pairings, female-female interactions are much more likely to occur across organizational boundaries. These findings have implications for research on homophily, gender, and formal and informal structure in organizations.