Located a few short blocks from the Plaza de Armas or Plaza Mayor Lima Center is the Convento de San Francisco which houses the largest catacombs in Peru.
The Convent is located about a five minute walk from the plaza de armas and is a fantastic attraction. The tour only costs about 10 soles each from what I recall and includes a complete tour of the convent as well as the catacombs below. A word of warning: as usual I recommend taking the spanish version of the tour is you have someone in your group which can assist you. Our kids took the spanish tour and it was twice as long and much more complete spending alot more time in the underground catacomb chambers.
They heard many secretes about the underground passages and alot more history including a tour of the library and upper level of the convent. The english tour was also informative and definitely a worthwhile visit.
Taking Pictures inside is not permitted. Please observe this rule as people remains are present.