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NOTE: Antidepressants also are known for negatively impacting sexual function. Increased seratonin is associated with decreased sexual desire for starters. In addition, the above study shows these drugs lower free testosterone levels as well. 
Regardless of short term affects on testosterone according to the studies, it is unlikely that these drugs will do anything but lower testosterone in the long term. Consider these risk factors for lower testosterone that are generally negatively impaced:1. Dopamine. Decreased levels of dopamine lead to sexual dysfunction and decreased sexual desire. This will likely lead to less sexual activity and less sexual activity will tend to decrease testosterone.
2. Diabetes and Metabolic Disorders. A significant risk factor for erectile dysfunction is type II (adult onset) diabetes. This is no surprise as diabetes is incredibly hard on the body and ages many tissues at an accelerated rate. The atypical antipsychotics are known to increase risk for diabetes.  Follow up research has verified this affect across a wide variety of the atypicals.  Blood sugar disorders will do nothing but lower testosterone, potentially total and free testosterone with time, due to the increased oxidative and inflammatory load placed on the body.
3. Prolactin. Elevated prolactin levels are a known libido killer in and of itself.  Again, this will tend to lead to decreased sex and sexual interest, which will probably lower testosterone long term (and even short term as mentioned above).
Therefore, long term studies my show other decreases in testosterone levels as well.
1) Journal of Clinical Psychopharmacology, 2002, 22:109-114, "The effects of anti-psychotic induced hyperprolactinaemia on the hypothalamic-pituitary-gonadal axis"
2) Neuroendocrinology Letters, Nos.1/2, Feb-Apr Vol.25, 2004, "Impact of a switch from typical to atypical antipsychotic drugs on quality of life and gonadal hormones in male patients with schizophrenia"
3) J Psychopharmacol, Jun 2007, 21(4):428-434, "The effect of chronic antipsychotic treatment on sexual behaviour, hormones and organ size in the male rat&http://priory.com/psych/sexdys.htm
5) Am J Psychiatry, Apr 2002, 159:561-566, "Association of Diabetes Mellitus With Use of Atypical Neuroleptics in the Treatment of Schizophrenia"
6) Psychopharmacol Bull, 2009; 42(1):1-21, "Atypical Antipsychotic Drugs and Diabetes Mellitus in the US Food and Drug Administration Adverse Event Database: A Systematic Bayesian Signal Detection Analysis"
7) Journal of Endocrinology, 2003, 179:357–365, "Effects of acute prolactin manipulation on sexual drive and function in males"
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