The Collaborative International Dictionary of English v.0.48:

Internally \In*ter"nal*ly\, adv.
   1. Inwardly; within the enveloping surface, or the boundary
      of a thing; within the body; beneath the surface.
      [1913 Webster]

   2. Hence: Mentally; spiritually. --Jer. Taylor.
      [1913 Webster]

WordNet (r) 3.0 (2006):

internally
    adv 1: on or from the inside; "an internally controlled
           environment" [ant: externally]

Moby Thesaurus II by Grady Ward, 1.0:

19 Moby Thesaurus words for "internally":
   by birth, by nature, centrally, congenitally, deeply, genetically,
   immanently, inly, innately, interiorly, intimately, intrinsically,
   inwardly, naturally, originally, primally, primitively, profoundly,
   under the surface