The Collaborative International Dictionary of English v.0.48:

Congenital \Con*gen"i*tal\ (k[o^]n*j[e^]n"[i^]*tal), a. [From
   Congenite.]
   Existing at, or dating from, birth; pertaining to one from
   birth; born with one; connate; constitutional; natural; as, a
   congenital deformity; a congenital liar. See Connate and
   native.

   Syn: connate; native; inborn; inherited; hereditary. [1913
        Webster +PJC]

The Collaborative International Dictionary of English v.0.48:

Native \Na"tive\ (n[=a]"t[i^]v), a. [F. natif, L. nativus, fr.
   nasci, p. p. natus. See Nation, and cf. Na["i]ve, Neif
   a serf.]
   1. Arising by birth; having an origin; born. [Obs.]
      [1913 Webster]

            Anaximander's opinion is, that the gods are native,
            rising and vanishing again in long periods of times.
                                                  --Cudworth.
      [1913 Webster]

   2. Of or pertaining to one's birth; natal; belonging to the
      place or the circumstances in which one is born; --
      opposed to foreign; as, native land, language, color,
      etc.
      [1913 Webster]

   3. Born in the region in which one lives; as, a native
      inhabitant, race; grown or originating in the region where
      used or sold; not foreign or imported; as, native
      oysters, or strawberries. In the latter sense, synonymous
      with domestic.
      [1913 Webster +PJC]

   4. Original; constituting the original substance of anything;
      as, native dust. --Milton.
      [1913 Webster]

   5. Conferred by birth; derived from origin; born with one;
      inherent; inborn; not acquired; as, native genius,
      cheerfulness, wit, simplicity, rights, intelligence, etc.
      Having the same meaning as congenital, but typically
      used for positive qualities, whereas congenital may be
      used for negative qualities. See also congenital
      [1913 Webster +PJC]

            Courage is native to you.             --Jowett
                                                  (Thucyd.).
      [1913 Webster]

   6. Naturally related; cognate; connected (with). [R.]
      [1913 Webster]

            the head is not more native to the heart, . . .
            Than is the throne of Denmark to thy father. --Shak.
      [1913 Webster]

   7. (Min.)
      (a) Found in nature uncombined with other elements; as,
          native silver, copper, gold.
      (b) Found in nature; not artificial; as native sodium
          chloride.
          [1913 Webster]

   Native American party. See under American, a.

   Native bear (Zool.), the koala.

   Native bread (Bot.), a large underground fungus, of
      Australia (Mylitta australis), somewhat resembling a
      truffle, but much larger.

   Native devil. (Zool.) Same as Tasmanian devil, under
      Devil.

   Native hen (Zool.), an Australian rail (Tribonyx
      Mortierii).

   Native pheasant. (Zool.) See Leipoa.

   Native rabbit (Zool.), an Australian marsupial (Perameles
      lagotis) resembling a rabbit in size and form.

   Native sloth (Zool.), the koala.

   Native thrush (Zool.), an Australian singing bird
      (Pachycephala olivacea); -- called also thickhead.

   Native turkey (Zool.), the Australian bustard (Choriotis
      australis); -- called also bebilya.
      [1913 Webster]

   Syn: Natural; natal; original; congenital.

   Usage: Native, Natural, Natal. natural refers to the
          nature of a thing, or that which springs therefrom;
          native, to one's birth or origin; as, a native
          country, language, etc.; natal, to the circumstances
          of one's birth; as, a natal day, or star. Native
          talent is that which is inborn; natural talent is that
          which springs from the structure of the mind. Native
          eloquence is the result of strong innate emotion;
          natural eloquence is opposed to that which is studied
          or artificial.
          [1913 Webster]

WordNet (r) 3.0 (2006):

congenital
    adj 1: present at birth but not necessarily hereditary; acquired
           during fetal development [syn: congenital, inborn,
           innate]

Moby Thesaurus II by Grady Ward, 1.0:

77 Moby Thesaurus words for "congenital":
   absolute, all-embracing, all-encompassing, all-out, all-pervading,
   atavistic, bodily, born, broad-based, clean, clear, coeval,
   comprehensive, connatal, connate, connatural, constitutional,
   consummate, deep-dyed, deep-seated, downright, dyed-in-the-wool,
   egregious, essential, exhaustive, genetic, hereditary,
   in the blood, inborn, inbred, incarnate, indigenous, indwelling,
   ingrained, inherited, innate, instinctive, instinctual, intensive,
   intrinsic, native, native to, natural, natural to, omnibus,
   omnipresent, organic, out-and-out, outright, perfect, pervasive,
   physical, plain, plumb, primal, pure, radical, regular, sheer,
   straight, sweeping, temperamental, thorough, thoroughgoing,
   through-and-through, total, ubiquitous, unacquired, unconditional,
   universal, unmitigated, unqualified, unreserved, unrestricted,
   utter, veritable, wholesale