The adverse effects of meditation as reported in scientific studies are as follows:

 - relaxation-induced anxiety and panic
 - paradoxical increases in tension
 - less motivation in life
 - boredom
 - pain
 - impaired reality testing
 - confusion and disorientation
 - feeling 'spaced out'
 - depression
 - increased negativity
 - being more judgmental
 - feeling addicted to meditation
 - uncomfortable kinaesthetic sensations
 - mild dissociation
 - feelings of guilt
 - psychosis-like symptoms
 - grandiosity
 - elation
 - destructive behavior
 - suicidal feelings
 - defenselessness
 - fear
 - anger
 - apprehension
 - despair

Also, anecdotal evidence suggests that meditation can worsen symptoms of some psychiatric problems.

Sources:

Study from 1992:
http://www.ncbi.nlm.nih.gov/pubmed/1428622
> Adverse effects of meditation: a preliminary investigation of
> long-term meditators, by Shapiro DH Jr.
> 
> Department of Psychiatry and Human Behavior, California College of Medicine, University of California, Irvine.
> 
> Abstract
> 
> Adverse effects of meditation were assessed in twenty-seven long term
> meditators (average 4.27 years) both retrospectively (time one) and
> prospectively at one month (time two) and six months (time three)
> following a meditation retreat. At both time one and time three
> subjects reported significantly more positive effects than negative
> from meditation. However, of the twenty-seven subjects, seventeen
> (62.9%) reported at least one adverse effect, and two (7.4%) suffered
> profound adverse effects. When subjects at time one were divided into
> three groups based on length of practice (16.7 months; 47.1 months;
> 105 months) there were no significant differences in adverse effects.
> How the data should be interpreted, and their implications both for
> the clinical and psychotherapeutic use of meditation as a
> relaxation/self-control strategy, and as a technique for facilitating
> personal and spiritual growth, are discussed. Limitations of the study
> and suggestions for future research are also offered.


Meta-analysis from 2000:
> Meditation: concepts, effects and uses in therapy by Alberto
> Perez-De-Albeniz and Jeremy Holmes
> 
> International Journal of Psychotherapy, Mar2000, Vol. 5 Issue 1,
> p49, 10p
>
> Abstract: This article reviews 75 scientific selected articles in the
> field of meditation, including Transcendental Meditation among others.
> It summarizes definitions of meditation, psychological and physiological
> changes, and negative side-effects encountered by 62.9% of meditators
> studied. While the authors did not restrict their study to TM, the
> side-effects reported were similar to those found in the "German
> Study" of Transcendental Meditators: relaxation-induced anxiety and
> panic; paradoxical increases in tension; less motivation in life;
> boredom; pain; impaired reality testing; confusion and disorientation;
> feeling 'spaced out'; depression; increased negativity; being more
> judgmental; feeling addicted to meditation; uncomfortable kinaesthetic
> sensations; mild dissociation; feelings of guilt; psychosis-like
> symptoms; grandiosity; elation; destructive behavior; suicidal
> feelings; defenselessness; fear; anger; apprehension; and despair.


Official recommendations in the US:
http://nccam.nih.gov/health/meditation/overview.htm#sideeffects
> Side Effects and Risks
> 
> Meditation is considered to be safe for healthy people. There have
> been rare reports that meditation could cause or worsen symptoms in
> people who have certain psychiatric problems, but this question has
> not been fully researched. People with physical limitations may not be
> able to participate in certain meditative practices involving physical
> movement. Individuals with existing mental or physical health
> conditions should speak with their health care providers prior to
> starting a meditative practice and make their meditation instructor
> aware of their condition.