Were there any Ph.D holders in American administrations apart from Kissinger and Condaleezza Rice?

Answer 1

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Woodrow Wilson is the only President to hold a Ph.D. (in Political Science from Johns Hopkins.)

As for Cabinet officers, doctorates are fairly common. (Kissinger and Rice probably made a bigger deal out of it than most.) In recent administrations you've had:

Obama: Steven Chu (Sec. of Energy - Ph.D. in Physics from Berkeley); Robert Gates (Sec. of Defense - Ph.D. from Georgetown in Russian History)

Bush: Robert Gates (see above); Condi Rice (Sec. of State; Ph.D. in Political Science from U. of Denver); Samuel Bodman (Sec. of Energy; Sc.D. in Chemical Engineering from M.I.T.)

Clinton: Madeleine Albright (State, Ph.D. in Public Affairs from Columbia); Lawrence Summers (Treasury; Ph.D. in Economics from MIT)