A common claim made by supporters of the HHS Mandate is that the mandate is rooted in science: Congress and the HHS tasked an objective scientific organization, the Institute of Medicine, with developing coverage recommendations; that group met, considered the evidence, and conveyed their coverage recommendations.
Except that’s not what happened . . . at least according to the IOM itself.
The IOM Report that forms the basis of the HHS Mandate for employers of 50 or more employees to provide no-copay coverage of all FDA-approved contraceptives explicitly disclaims having considered most of the factors that go into intelligent insurance coverage recommendations. The committee that wrote the report understood its charge to focus on clinical efficacy; its assessments of what preventive services should be considered by HHS were rooted in guidance provided for primary caregivers and patients. The committee explicitly noted, by contrast, that “[c]overage decisions often consider a host of other issues, such as established practices; patient and clinician preferences; availability; ethical, legal, and social issues; and availability of alternatives.” [pp. 6-7, emphases added] In developing the IOM recommendations, “cost-effectiveness was explicitly excluded as a factor that the committee could use in developing recommendations, and so the committee process could not evaluate preventive services on this basis.” 
The 250-page report issued by the IOM not only explicitly disclaims coverage recommendations, but also chides the dissenting member of the committee for suggesting that the committee failed to consider how its report would be misused in formulating coverage recommendations. Rather than counter the dissent’s statement that the IOM report’s recommendations were based in large part on task force recommendations that “were never intended to provide a basis for insurance coverage determinations” [233, App. D], the majority of the committee noted that “cost considerations were outside the scope of the [committee's] charge,” and that “HHS . . . may consider other factors including cost in its development of coverage decisions.” [235, App. D.]
All of this matters a great deal when evaluating claims about the government’s interest in forcing employers of 50 or more full-time employees to provide no-copay coverage of all FDA-approved contraceptives. The IOM report does not purport to address the relationship between no-copay insurance coverage of contraceptives and unintended pregnancy. The report cites some studies about related issues. But the report contains no evidence about the effect that the required coverage would have on the health outcomes of the relevant population.
To the contrary, the dissenting opinion notes–without contravention–that the extent to which “coverage of preventive service leads to a reduction in healthcare expenditure depends on the fraction of enrollees using the service before the service becomes covered and the magnitude of the response among enrollees who experience the reduction in out-of-pocket price.” [234 App. D.] This is common sense. If employees are using contraception because the benefits outweigh the costs regardless of insurance coverage, then their usage will not change once no-copay employer coverage is added. Instead, usage will remain constant and the mandate will only shift costs. The IOM report contains no discussion of cost-benefit considerations specific to mandated contraceptives coverage for women with full-time employment and benefits provided by an employer of fifty or more FTEs.
The problem for the government is even more acute in the cases brought by employers who offer group health plans that include no-copay coverage for most contraceptives and exclude only abortion-causing drugs and devices. The magnitude of any change in contraceptive use with and without those coverage must be really low. I have not seen any evidence (is there any?), but it is hard to believe that a woman with full-time employment and health benefits who has no-copay access to all other contraceptives will access emergency contraception (available over the counter for $40-$50) at a significantly lower rate than other women due to her employer’s lack of no-copay coverage for that back-up method of birth control.
None of this is to deny that the IOM Report is based in science. But that science is limited to clinical efficacy. And nobody disputes that FDA-approved contraceptives are clinically efficacious in reducing unintended pregnancy. That is not what the dispute is about. The dispute, rather, is about an insurance mandate. And the IOM Report simply does not speak to issues of cost and coverage. To invoke the IOM Report in response to conscience claims against the IOM-derived insurance mandate is not to fight fire with fire, but to drown conscience in con science.